Methods in Ecology and Evolution

Article	Citations
	392
Cover Picture and Issue Information	156
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Cover Picture and Issue Information	94
A network theoretic method for the basic reproductive number for infectious diseases	91
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	80
FlywayNet : A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	77
A new centrality index designed for multilayer networks	62
Beneath the buzz: Quantifying nest locations and densities of ground‐nesting wild bees (Hymenoptera: Anthophila)	60
State‐space models and inference approaches for aquatic animal tracking with passive acoustic telemetry and biologging sensors	58
Filtering heart rates using data densities: The boxfilter R package	58
Toward a unified approach to modelling adaptation among demographers and evolutionary ecologists	57
Inferring state‐dependent diversification rates using approximate Bayesian computation	55
Individualised niches in a variable environment—Consequences for environmental change responses	55
occupancyTuts : Occupancy modelling tutorials with RPresence	54
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	54
Exploring congruent diversification histories with flexibility and parsimony	53
AF‐vapeR : A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	52
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	49
Goby gummies: A customizable and edible assay to quantify predation in aquatic ecosystems	49
Forking anatomy: How MorphoDepot applies the open‐source development model to 3D digital morpholog	48
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	45

From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA ( eDNA	44
ECOGEN : Bird sounds generation using deep learning	44
Empirical dynamic programming for model‐free ecosystem‐based management	44
Individual tree extraction through 3D promptable segmentation networks	43
How to get the most out of phylogenetic imputation without abusing it	42
Nighthawk : Acoustic monitoring of nocturnal bird migration in the Americas	42
BATScan: A radar classification tool reveals large‐scale bat migration patterns	41
A pluralistic framework for measuring, interpreting and decomposing heterogeneity in meta‐analysis	41
Using cloud radar to investigate the effect of rainfall on migratory insect flight	41
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity	40
Classifying the activity states of small vertebrates using automated VHF telemetry	39
A general framework for jointly modelling thermal and hydric constraints on developing eggs	38
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study	38
Multi‐trait point pattern reconstruction of plant ecosystems	38
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	38
‘But I can't preregister my research’: Improving the reproducibility and transparency of ecology and conservation with adaptive preregistration for model‐based research	37
Data reconciliation in multi‐trait experiments with kinship ordination	37
Integrated movement models for individual tracking and species distribution data	37
EcoEnsemble: A general framework for combining ecosystem models in R	36
M oon S hine : A software‐hardware system for simulating moonlight ground illuminance and re‐creat	34
A 3D modelling approach to measuring structural characteristics of bird nest interiors	34
Benchmarking imputation methods for categorical biological data	33
The ecological forecast limit revisited: Potential, absolute and relative system predictability	33
Towards ‘digital ecology’: Advances in integrating artificial intelligence from data generation to ecological insight	33
Cover Picture and Issue Information	32
Scalable semantic 3D mapping of coral reefs with deep learning	32
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lacunr: Efficient 3D lacunarity for voxelized LiDAR data from forested ecosystems	32
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	32
Towards biologically realistic estimates of home range and spatial exposure for colonial animals	32
A global estimator of C and N isotope baselines for fresh waters	31
TinyCO 2 : High‐performance, low‐cost CO	31
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors	31
Microclimf: Fast modelling of microclimate across real landscapes in R	31
Using standardized fish‐specific autonomous reef monitoring structures ( FARMS ) to quantify cryptobenthic fish communities	31
When to monitor or control: Informed invasive species management using a partially observable Markov decision process ( POMDP ) framework	31
The Benthic Underwater Microscope imaging PAM ( BUMP ): A non‐invasive tool for in situ assessment	30
Retrodiction of forest demography: Backward simulation with reverse matrix models	30
An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms	30
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems	29
Trait coevolution and causal inference using generalized dynamic phylogenetic models	29
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens	29
PleistoDist : A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos	28
Detecting and reducing heterogeneity of error in acoustic classification	28
Same data, different results? Machine learning approaches in bioacoustics	28
Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches	28
treats: A modular R package for simulating trees and traits	28
qad : An R‐package to detect asymmetric and directed dependence in bivariate samples	27
A Double machine learning trend model for citizen science data	27
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities	27

Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology	27
Cover Picture and Issue Information	26
A wireless, remotely operable and easily customizable robotic flower system	26
RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification	26
Sensors versus surveyors: Comparing passive acoustic monitoring, camera trapping and observer‐based monitoring for terrestrial mammals	26
A terrestrial laser scanning‐based workflow for component‐wise estimation of individual tree above‐ground biomass	26
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface	26
Contrastive ecoacoustic indices: Large‐scale global soundscape characterization with contrastive inference	26
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies	26
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES	26
Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data	26
Data‐driven discovery of mechanistic ecosystem models with LLMs	25
The CV is dead, long live the CV !	25
A short guide for effective field data collection	25
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks	25
Addressing spatial confounding in geostatistical regression models: An R‐ INLA approach	24
Vegetation patterns pinpoint the least resilient dryland sites	24
Correction to: Quantifying degradation in animal acoustic signals with the R package baRulho	24
Novel class identification: A human‐in‐the‐loop approach for efficient species recognition in bioacoustic data	23
TreeCompR : Tree competition indices for inventory data and 3D point clouds	23
The power of forecasts to advance ecological theory	23
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling	23
Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all	23
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species	23
Residual diagnostics for assessing closed population capture–recapture models	23
OpenSoundscape: An open‐source bioacoustics analysis package for Python	23
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning	23
sound C lass : An automatic sound classification tool for biodiversity monitoring using machine learning	22
Animal geolocation with convolution algorithms in Julia and R via Wahoo.jl	22
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Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species	22
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes	22
poolHelper : An R package to help in designing Pool‐Seq studies	22
Paying attention to other animal detections improves camera trap classification models	22
Impact of sampling strategy on inference of community assembly processes in phylogenetic island biogeography	21
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent	21
COPIS : A robust and versatile robotic imaging system for the 3D digitization of natural history specimens with photog	21
Reconstructing Langevin systems from high‐ and low‐resolution time series using Euler and Hermite reconstructions	21
ipsecr: An R package for awkward spatial capture–recapture data	21
Synthesizing forecasts to inform decision‐making and advance ecological theory	21
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	21
NAPS : Integrating pose estimation and tag‐based tracking	20
ForestForTrees : An R package to infer forest structure from remote sensing data	20
Understanding variability and complexity of airborne fungal eDNA	20
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Practical guidelines and the EMLN R package for handling ecological multilayer networks	20
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset	20
Estimating interaction strengths for diverse horizontal systems using performance data	20
DeepDiveR—A software for deep learning estimation of palaeodiversity from fossil occurrences	20
tidysdm : Leveraging the flexibility of tidymodels for species distribution modelling in R	20
Methods to account for incomplete viewsheds in distance sampling	19
Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees	19
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Towards scalable insect monitoring: Ultra‐lightweight CNNs as on‐device triggers for insect camera traps	19
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements	19
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	19
Cover Picture and Issue Information	19
sabinaNSDM : An R package for spatially nested hierarchical species distribution modelling	19
Guidelines for the prediction of species interactions through binary classification	19
Cover Picture and Issue Information	19
A conceptual framework for host‐associated microbiomes of hybrid organisms	19
Modelling approaches for meta‐analyses with dependent effect sizes in ecology and evolution: A simulation study	18
Correction to ‘The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems’	18
Correction to ‘An evaluation of multi‐species occupancy models with correlated species occurrences’	18
A framework for post‐processing bird tracks from automated tracking radar systems	18
Computationally efficient Bayesian capture–mark–recapture models with transients, applied to survival of hand‐reared African Penguins	18
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs	18
A GLMM approach for combining multiple relative abundance surfaces	18
Estimating spatiotemporal reproductive dynamics of fish populations with passive acoustic monitoring: A state‐space model approach	18
Rapid construction of insect–plant interaction networks via multiplexed long‐fragment DNA metabarcoding and NGS	18
Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids	18
Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements	18
Long‐term collar deployment leads to bias in soil respiration measurements	18
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products	17
A low‐cost IoT network to monitor microclimate variables in ecosystems	17
Pitfalls arising from site selection bias in population monitoring defy simple heuristics	17
Advancing aquatic biodiversity assessments of invertebrates using eDNA metabarcoding: A systematic evaluation of primers for marine and freshwater co	17
Studying collective animal behaviour with drones and computer vision	17

The persistent advantage of model‐based phylogenetic methods for single‐trait prediction	17
RAPID: Real‐time animal pattern re‐identification on edge devices, an open‐source tool for field deployment	17
Improved order selection method for hidden Markov models: A case study with movement data	17
Extending isolation by resistance to predict genetic connectivity	17
A novel generalized spatial mark‐resight model that accounts for group associations	17
Non‐invasive reconstruction of complete mitochondrial genomes from aquatic environmental DNA using PCR‐free long‐read sequencing	17
Acoustic and archival technologies join forces: A combination tag	17
PiCAM : A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments	16
Applying the maximum entropy principle to neural networks enhances multi‐species distribution models	16
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Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data	16
Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa	16
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3D photogrammetry as a low‐cost and non‐invasive method for acoustic modelling of animal hearing	16
Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring	16
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ChirpArray : A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	15
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CATS : A high‐performance software framework for simulating plant migration in changing environments	15
Time‐lapse cameras bridge the gap between remote sensing and in situ observations of tundra phenology	15
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	15
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	15
PoolDilutionR : An R package for easy optimization of isotope pool dilution calculations	15
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Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	15
Sap Flow Analyzer : A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	15
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	15
One number to rule them all: The Wildlife Sperm Index for standardized gamete assessment	15
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	15
Correction to ‘ PhyBaSE : A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses’	15
Clustering and unconstrained ordination with Dirichlet process mixture models	15
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	15
Generating continuous maps of genetic diversity using moving windows	15
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Realising the promise of large data and complex models	14
Investigating soil mesofauna cryptic diversity: Current challenges and perspectives	14
theRmalUAV: An R package to clean and correct thermal UAV data for accurate land surface temperatures	14
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	14
Quantifying macro‐evolutionary patterns of trait mean and variance with phylogenetic location–scale models	14
ENphylo : A new method to model the distribution of extremely rare species	14
Connectivity conservation planning through deep reinforcement learning	14
ohun: An R package for diagnosing and optimizing automatic sound event detection	13
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	13
Bioregionalization analyses with the bioregion R package	13
Predicting ecological interactions across space through pairwise integration of latent network patterns	13
HSC 3 D : A Python package to quantify three‐dimensional habitat structural complexity	13
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Beyond the next step: A multi‐criteria generative validation framework for step selection functions	13
Home‐range spillover in habitats with impassable boundaries: Causes, biases and corrections using autocorrelated kernel density estimation	13
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R	13
A new tool to improve the estimates of interaction rewiring considering the whole community composition	13
Ten practical guidelines for microclimate research in terrestrial ecosystems	13
Impact of acoustic index parameters on soundscape comparisons	13
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	13
metaRange : A framework to build mechanistic range models	13
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	13
Robust passive sampling of airborne environmental DNA to monitor plants and animals	13
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	13
An intuitive method to calculate the utilization distribution of an animal from step‐selection analysis	13
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	13
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mpmsim: An R package for simulating matrix population models	13
plantTracker : An R package to translate maps of plant occurrence into demographic data	13
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	12
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	12
Simple assay quantifying sediment resuspension effects on marine carbon storage	12
patter: Particle algorithms for animal tracking in R and Julia	12
A new method for voxel‐based modelling of three‐dimensional forest scenes with integration of terrestrial and airborne LiDAR data	12
USE it: Uniformly sampling pseudo‐absences within the environmental space for applications in habitat suitability models	12
Discovering the unseen: A performance comparison of taxonomic classification methods for unknown DNA barcodes	12
Distinguishing passive and driven trait evolution in the presence of boundaries	12
Avoiding confusion: Modelling image identification surveys with classification errors	12
Fine‐scale reconstruction of pelagic fish migration by iso‐logging of eye lens	12
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	12
Geolocation with a magnetic sensor	11
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Detecting stochasticity in population time series using a non‐parametric test of intrinsic predictability	11
Deep reinforcement learning for conservation decisions	11
Fieldwork in conservation organisations–A review of methodological challenges, opportunities and ethics	11
Adaptive sampling in ecology: Key challenges and future opportunities	11
Integrating eco‐evolutionary dynamics into matrix population models for structured populations: Discrete and continuous frameworks	11
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Mitigating pseudoreplication and bias in resource selection functions with autocorrelation‐informed weighting	11
Coupling gel electrophoresis with photoluminescence reveals biochrome complexes in modern and fossil shells	11
Resin‐coated urea effectively simulates the chronic dynamics of natural nitrogen deposition	11
dentist: Quantifying uncertainty by sampling points around maximum likelihood estimates	11
DImodelsMulti: An R package for fitting Diversity‐Interactions models to repeated measures or multivariate data	11
EEMtoolbox : A user‐friendly R package for flexible ensemble ecosystem modelling	11
Systematic review and best practices for drone remote sensing of invasive plants	11
High‐magnification platform for characterising microscopic communities	11
Introduction to deep learning methods for multi‐species predictions	11
Know what you don't know: Embracing state uncertainty in disease‐structured multistate models	11
Spatial close‐kin mark‐recapture models applied to terrestrial species with continuous natal dispersal	10
A calibration framework to improve mechanistic forecasts with hybrid dynamic models	10